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Budhbaware T, Rathored J, Shende S. Molecular methods in cancer diagnostics: a short review. Ann Med 2024; 56:2353893. [PMID: 38753424 PMCID: PMC11100444 DOI: 10.1080/07853890.2024.2353893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required. OBJECTIVE In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer. METHODS We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria. RESULTS The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes. LIMITATION The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field. CONCLUSION After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.
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Affiliation(s)
- Tanushree Budhbaware
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Jaishriram Rathored
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Sandesh Shende
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
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Kakooza S, Eneku W, Nabatta E, Wampande EM, Ssajjakambwe P, Wanyana M, Munyiirwa DFN, Ndoboli D, Namuyinda D, Athieno G, Kayaga E, Okwasiimire R, Tsuchida S, Ushida K, Sakurai K, Mutebi F. Integrating multi-wet laboratory diagnostics to study staphylococci in animals in Uganda. BMC Microbiol 2024; 24:298. [PMID: 39127665 DOI: 10.1186/s12866-024-03442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Several diagnostic environments in Uganda lack real-time, robust and high-throughput technologies for comprehensive typing of microbes, which is a setback to infectious disease surveillance. This study combined various wet laboratory diagnostics to understand the epidemiology of pathogenic staphylococci isolated from animals in Uganda and the implications for global health security priorities. METHODS A retrospective study was conducted employing records and pathogenic staphylococci (from animals) archived at the Central Diagnostic Laboratory (CDL), Makerere University, Uganda, between January 2012 and December 2019. The bacteria were speciated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and tested for virulence factors [beta lactamases, lecithinase, deoxyribonuclease (DNase), haemolysins] and resistance to ten antimicrobials of clinical and veterinary relevance. Tetracycline and methicillin resistance genes were also tested. RESULTS The prevalent diseases were mastitis in cattle and skin infections in dogs. Of the 111 staphylococci tested by MALDI-TOF MS, 79 (71.2%) were Staphylococcus aureus, 27 (24.3%) were Staphylococcus pseudintermedius and 5 (4.5%) were Staphylococcus schleiferi. All these strains expressed haemolysins. The prevalence of strains with lecithinase, penicillinase, cephalosporinase and DNase was 35.9% (14/39), 89.7% (35/39), 0.0% (0/39) and 87.2% (34/39), respectively. Staphylococci were primarily resistant to early penicillins (over 80%), tetracycline (57.7%), and chloramphenicol (46.2%). Minimal resistance was noted with cloxacillin (0.0%), ciprofloxacin (9.6%), and cefoxitin (3.8%). The prevalence of multidrug resistance (MDR) was 78.8% for general staphylococci, 82.2% for S. aureus, 73.1% for S. pseudintermedius, and 60.0% for S. schleiferi. Multidrug resistant staphylococci were significantly more prevalent in the cattle isolates than in the dog isolates (P < 0.05). The prevalence of methicillin-resistant staphylococci (MRS) tested by resistance to cefoxitin and mecA carriage was 3.8%. These four strains were all isolated from dog skin infections. The tetK gene was the most predominant (35.4%), followed by tetM (25.0%). CONCLUSION In resource-constrained settings, the approach of integrated diagnostics promises sustainable disease surveillance and the addressing of current capacity gaps. The emergence of MRS (zoonotic bacteria) in companion animals creates a likelihood of reduced treatment options for related human infections, a threat to global health.
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Affiliation(s)
- Steven Kakooza
- Central Diagnostic Laboratory, College of Veterinary medicine, Animal resources and Biosecurity, Makerere University, Kampala, Uganda.
| | - Wilfred Eneku
- Department of Veterinary Pharmacy, Clinics and Comparative Medicine, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
| | - Esther Nabatta
- National Animal Disease Diagnostic and Epidemiology Centre, Entebbe, Uganda
| | - Eddie M Wampande
- Department of Veterinary Pharmacy, Clinics and Comparative Medicine, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
| | - Paul Ssajjakambwe
- Department of Veterinary Pharmacy, Clinics and Comparative Medicine, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
| | - Mariam Wanyana
- Central Diagnostic Laboratory, College of Veterinary medicine, Animal resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Damien F N Munyiirwa
- Central Diagnostic Laboratory, College of Veterinary medicine, Animal resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Dickson Ndoboli
- Central Diagnostic Laboratory, College of Veterinary medicine, Animal resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Dorcus Namuyinda
- Central Diagnostic Laboratory, College of Veterinary medicine, Animal resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Grace Athieno
- Central Diagnostic Laboratory, College of Veterinary medicine, Animal resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Edrine Kayaga
- Central Diagnostic Laboratory, College of Veterinary medicine, Animal resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Rodney Okwasiimire
- Central Diagnostic Laboratory, College of Veterinary medicine, Animal resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Sayaka Tsuchida
- College of Bioscience and Biotechnology, Biotechnolorere University, Aichi, Japan
| | - Kazunari Ushida
- College of Bioscience and Biotechnology, Biotechnolorere University, Aichi, Japan
| | - Ken'ichi Sakurai
- Faculty of Life and Environmental Sciences, Department of Animal Sciences, Teikyo University of Science, Tokyo, Japan
| | - Francis Mutebi
- Central Diagnostic Laboratory, College of Veterinary medicine, Animal resources and Biosecurity, Makerere University, Kampala, Uganda
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Mahmoudi A, Jalili A, Butler AE, Aghaee-Bakhtiari SH, Jamialahmadi T, Sahebkar A. Exploration of the Key Genes Involved in Non-alcoholic Fatty Liver Disease and Possible MicroRNA Therapeutic Targets. J Clin Exp Hepatol 2024; 14:101365. [PMID: 38433957 PMCID: PMC10904918 DOI: 10.1016/j.jceh.2024.101365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024] Open
Abstract
Background MicroRNAs (miRNAs) are promising therapeutic agents for non-alcoholic fatty liver disease (NAFLD). This study aimed to identify key genes/proteins involved in NAFLD pathogenesis and progression and to evaluate miRNAs influencing their expression. Methods Gene expression profiles from datasets GSE151158, GSE163211, GSE135251, GSE167523, GSE46300, and online databases were analyzed to identify significant NAFLD-related genes. Then, protein-protein interaction networks and module analysis identified hub genes/proteins, which were validated using real-time PCR in oleic acid-treated HepG2 cells. Functional enrichment analysis evaluated signaling pathways and biological processes. Gene-miRNA interaction networks identified miRNAs targeting critical NAFLD genes. Results The most critical overexpressed hub genes/proteins included: TNF, VEGFA, TLR4, CYP2E1, ACE, SCD, FASN, SREBF2, and TGFB1 based on PPI network analysis, of which TNF, TLR4, SCD, FASN, SREBF2, and TGFB1 were up-regulated in oleic acid-treated HepG2 cells. Functional enrichment analysis for biological processes highlighted programmed necrotic cell death, lipid metabolic process response to reactive oxygen species, and inflammation. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, the highest adjusted P-value signaling pathways encompassed AGE-RAGE in diabetic complications, TNF, and HIF-1 signaling pathways. In gene-miRNA network analysis, miR-16 and miR-124 were highlighted as the miRNAs exerting the most influence on important NAFLD-related genes. Conclusion In silico analyses identified NAFLD therapeutic targets and miRNA candidates to guide further experimental investigation.
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Affiliation(s)
- Ali Mahmoudi
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Iran
| | - Amin Jalili
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Iran
| | | | - Seyed H. Aghaee-Bakhtiari
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Iran
- Bioinformatics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tannaz Jamialahmadi
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Martorelli I, Pooryousefi A, van Thiel H, Sicking FJ, Ramackers GJ, Merckx V, Verbeek FJ. Multiple graphical views for automatically generating SQL for the MycoDiversity DB; making fungal biodiversity studies accessible. Biodivers Data J 2024; 12:e119660. [PMID: 38933486 PMCID: PMC11199959 DOI: 10.3897/bdj.12.e119660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Fungi is a highly diverse group of eukaryotic organisms that live under an extremely wide range of environmental conditions. Nowadays, there is a fundamental focus on observing how biodiversity varies on different spatial scales, in addition to understanding the environmental factors which drive fungal biodiversity. Metabarcoding is a high-throughput DNA sequencing technology that has positively contributed to observing fungal communities in environments. While the DNA sequencing data generated from metabarcoding studies are available in public archives, this valuable data resource is not directly usable for fungal biodiversity investigation. Additionally, due to its fragmented storage and distributed nature, it is not immediately accessible through a single user interface. We developed the MycoDiversity DataBase User Interface (https://mycodiversity.liacs.nl) to provide direct access and retrieval of fungal data that was previously inaccessible in the public domain. The user interface provides multiple graphical views of the data components used to reveal fungal biodiversity. These components include reliable geo-location terms, the reference taxonomic scientific names associated with fungal species and the standard features describing the environment where they occur. Direct observation of the public DNA sequencing data in association with fungi is accessible through SQL search queries created by interactively manipulating topological maps and dynamic hierarchical tree views. The search results are presented in configurable data table views that can be downloaded for further use. With the MycoDiversity DataBase User Interface, we make fungal biodiversity data accessible, assisting researchers and other stakeholders in using metabarcoding studies for assessing fungal biodiversity.
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Affiliation(s)
- Irene Martorelli
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
- Naturalis Biodiversity Center, Leiden, NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
| | - Aram Pooryousefi
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
| | - Haike van Thiel
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
| | - Floris J Sicking
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
| | - Guus J Ramackers
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
| | - Vincent Merckx
- Naturalis Biodiversity Center, Leiden, NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, NetherlandsInstitute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdamNetherlands
| | - Fons J Verbeek
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, NetherlandsLeiden Institute of Advanced Computer Science (LIACS), Leiden UniversityLeidenNetherlands
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Wang Y, Wang T, Ma T, Zhao J, Qi W. Shexiang tongxin dropping pill alleviates myocardial injury induced by coronary microembolization by down-regulating APOC1 to inhibit STAT3 signaling pathway. Aging (Albany NY) 2024; 16:8484-8496. [PMID: 38771126 PMCID: PMC11164485 DOI: 10.18632/aging.205796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 03/03/2024] [Indexed: 05/22/2024]
Abstract
AIM This study determines to validate the mechanism of Shexiang Tongxin dropping pill (STDP) in attenuating coronary microembolization (CME) induced myocardial injury. METHODS CME rat models were established and underwent corresponding treating. Gene chip analysis was performed in rat myocardial tissues for GO and KEGG enrichment analysis. The differentially expressed genes were detected by qRT-PCR. H&E staining and ELISA were used for pathological analysis and detection of troponin (cTnI) and Creatine Kinase Isoenzyme (CK-MB). Lipopolysaccharide (LPS) treated primary cardiomyocytes were used to mimic inflammatory in vitro models. Cell viability and apoptosis of cardiomyocytes were determined by MTT and flow cytometry. The expressions of inflammatory cytokines, apoptotic proteins and proteins related to the STAT3 signal pathway were detected by western blot. APOC1 mRNA expression was detected by qRT-PCR. Immunofluorescence (IF) was used for subcellular localization of p-STAT3 and the binding of APOC1 with STAT3 was verified using Co-IP. RESULTS STDP can attenuate myocardial injury in CME rat models, and lead to decreased expression of APOC1 and suppressed STAT3 signal pathway. In vitro models found STDP can suppress the cell viability and cell apoptosis of primary cardiomyocytes, in addition to suppressing the secretions of IL-6, IL-1β and TNF-α, while the protective effect of STDP can be reversed by overexpression of APOC1. Co-IP found that APOC1 can bind STAT3 directly. APOC1 can increase p-STAT3 expression in the nucleus to activate the STAT3 signal pathway. CONCLUSIONS STDP can suppress APOC1 and STAT3 signal pathway to inhibit inflammation and cell apoptosis of cardiomyocytes. APOC1 may be one of the key regulatory factors in CME-induced myocardial injury.
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Affiliation(s)
- Yangui Wang
- Department of General Practice, Shanghai Pudong New Area People’s Hospital, Pudong New Area 201299, Shanghai, P.R. China
| | - Tao Wang
- Department of General Practice, Shanghai Pudong New Area People’s Hospital, Pudong New Area 201299, Shanghai, P.R. China
| | - Tingting Ma
- Department of General Practice, Shanghai Pudong New Area People’s Hospital, Pudong New Area 201299, Shanghai, P.R. China
| | - Jin Zhao
- Department of General Practice, Shanghai Pudong New Area People’s Hospital, Pudong New Area 201299, Shanghai, P.R. China
| | - Weigang Qi
- Department of General Practice, Shanghai Pudong New Area People’s Hospital, Pudong New Area 201299, Shanghai, P.R. China
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Thapa R, Afzal M, Goyal A, Gupta G, Bhat AA, Almalki WH, Kazmi I, Alzarea SI, Shahwan M, Kukreti N, Ali H, Dureja H, Kumar P, Singh TG, Kuppusamy G, Singh SK, Dua K. Exploring ncRNA-mediated regulation of EGFR signalling in glioblastoma: From mechanisms to therapeutics. Life Sci 2024; 345:122613. [PMID: 38582393 DOI: 10.1016/j.lfs.2024.122613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Glioblastoma (GBM) is the most prevalent and deadly primary brain tumor type, with a discouragingly low survival rate and few effective treatments. An important function of the EGFR signalling pathway in the development of GBM is to affect tumor proliferation, persistence, and treatment resistance. Advances in molecular biology in the last several years have shown how important ncRNAs are for controlling a wide range of biological activities, including cancer progression and development. NcRNAs have become important post-transcriptional regulators of gene expression, and they may affect the EGFR pathway by either directly targeting EGFR or by modifying important transcription factors and downstream signalling molecules. The EGFR pathway is aberrantly activated in response to the dysregulation of certain ncRNAs, which has been linked to GBM carcinogenesis, treatment resistance, and unfavourable patient outcomes. We review the literature on miRNAs, circRNAs and lncRNAs that are implicated in the regulation of EGFR signalling in GBM, discussing their mechanisms of action, interactions with the signalling pathway, and implications for GBM therapy. Furthermore, we explore the potential of ncRNA-based strategies to overcome resistance to EGFR-targeted therapies, including the use of ncRNA mimics or inhibitors to modulate the activity of key regulators within the pathway.
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Affiliation(s)
- Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, Mathura, U.P., India
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
| | - Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Aljouf 72341, Saudi Arabia
| | - Moyad Shahwan
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates; Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, 346, 7, United Arab Emirates
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Ghudda, Punjab, India
| | - Thakur Gurjeet Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India
| | - Gowthamarajan Kuppusamy
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, India
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia
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Zhao X, Li X, Miao Z. Identification and validation of regulatory T cell-associated gene signatures to predict colon adenocarcinoma prognosis. Int Immunopharmacol 2024; 132:112034. [PMID: 38588631 DOI: 10.1016/j.intimp.2024.112034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/17/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Colon adenocarcinoma (COAD) is a common cause of cancer-related death. Due to the difficulty in early diagnosis and drug resistance, conventional treatments are difficult to be effective. Some studies have found that the functional recovery of T cells in the tumor microenvironment, especially regulatory T cells (Tregs), plays an important role in the progression of cancer. This study used the TCGA data set, clinical information and RNA-seq data of COAD patients to construct a Tregs-related risk score (TRS) through methods such as WGCNA, single-factor Cox, multi-factor Cox and random survival forest (RSF). Moreover, we also used the TCGA test set and internal validation set to verify the predictive ability of TRS, and used functional enrichment analysis and somatic mutation analysis to mine genes related to TRS, such as like thrombin/trypsin receptor 2 (F2RL2), inhibin subunit beta B (INHBB) and melanoma antigen family A12 (MAGEA12). Moreover, this study confirmed the expression of these prognostic genes using scRNA-seq data. We also performed qPCR analysis of various genes in normal and cancerous colon cancer cell lines to verify that these genes indeed play a role in CODA patients. We also constructed a mouse CODA model to study and evaluate the impact of key genes such as MAGEA12 on tumor growth in mice. This study explores the important role of Treg cells in the prognosis of COAD and discovers some potential biomarkers for the occurrence and development of COAD, which provides some new ideas for the treatment of COAD.
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Affiliation(s)
- Xiaomeng Zhao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Xuanwen Li
- Department of Nutritional, Tianjin Beichen Hospital of Chinese Medicine, Tianjin, PR China
| | - Zhi Miao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China.
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Thuma TBT, Procopio RA, Jimenez HJ, Gunton KB, Pulido JS. Hypomorphic variants in inherited retinal and ocular diseases: A review of the literature with clinical cases. Surv Ophthalmol 2024; 69:337-348. [PMID: 38036193 DOI: 10.1016/j.survophthal.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
Hypomorphic variants decrease, but do not eliminate, gene function via a reduction in the amount of mRNA or protein product produced by a gene or by production of a gene product with reduced function. Many hypomorphic variants have been implicated in inherited retinal diseases (IRDs) and other genetic ocular conditions; however, there is heterogeneity in the use of the term "hypomorphic" in the scientific literature. We searched for all hypomorphic variants reported to cause IRDs and ocular disorders. We also discuss the presence of hypomorphic variants in the patient population of our ocular genetics department over the past decade. We propose that standardized criteria should be adopted for use of the term "hypomorphic" to describe gene variants to improve genetic counseling and patient care outcomes.
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Affiliation(s)
- Tobin B T Thuma
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA, USA
| | | | - Hiram J Jimenez
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA, USA
| | - Kammi B Gunton
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA, USA
| | - Jose S Pulido
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA, USA; Retina Service, Wills Eye Hospital, Philadelphia, PA, USA.
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Sun L, Wang J, Lei J, Zhang Y, Zhang Y, Zhang Y, Xing S. Differential gene expression and miRNA regulatory network in coronary slow flow. Sci Rep 2024; 14:8419. [PMID: 38600259 PMCID: PMC11006858 DOI: 10.1038/s41598-024-58745-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
Coronary slow flow (CSF) is characterized by slow progression of coronary angiography without epicardial stenosis. The aim of this study was to explore the potential biomarkers and regulatory mechanism for CSF. Peripheral blood mononuclear cells from 3 cases of CSF and 3 healthy controls were collected for high-throughput sequencing of mRNA and miRNA, respectively. The differentially expressed mRNAs (DE-mRNAs) and miRNAs (DE-miRNAs) was identified. A total of 117 DE-mRNAs and 32 DE-miRNAs were obtained and they were mainly enriched in immune and inflammatory responses. Twenty-six DE-mRNAs were the predicted target genes for miRNAs by RAID, and then the regulatory network of 15 miRNAs were constructed. In addition, through the PPI network, we identified the three genes (FPR1, FPR2 and CXCR4) with larger degrees as hub genes. Among them, FPR1 was regulated by hsa-miR-342-3p, hsa-let-7c-5p and hsa-miR-197-3p and participated in the immune response. Finally, we validated the differential expression of hub genes and key miRNAs between 20 CSF and 20 control. Moreover, we found that miR-342-3p has a targeted regulatory relationship with FPR1, and their expression is negatively correlated. Then we established a hypoxia/reoxygenation (H/R) HUVEC model and detected FPR1, cell proliferation and apoptosis. Transfection with miR-342-3p mimics can significantly promote the proliferation of HUVEC under H/R conditions. FPR1 were associated with CSF as a biomarker and may be regulated by miR-342-3p potential biomarkers.
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Affiliation(s)
- Lihua Sun
- Department of Cardiology, Zhongshan Boai Hospital Affiliated to South Medical University, No. 6, Chenggui Road, Zhongshan, 528405, Guangdong, China
| | - Juan Wang
- Department of Cardiology, The Fifth Affiliated Hospital of Xinjiang Medical University, No. 118 Henan West Road, Xinshi District, Urumqi, 830000, Xinjiang, China
| | - Jimin Lei
- Department of Cardiology, Zhongshan Boai Hospital Affiliated to South Medical University, No. 6, Chenggui Road, Zhongshan, 528405, Guangdong, China
| | - Ying Zhang
- Department of Cardiology, The Fifth Affiliated Hospital of Xinjiang Medical University, No. 118 Henan West Road, Xinshi District, Urumqi, 830000, Xinjiang, China
| | - Yue Zhang
- Department of Cardiology, The Fifth Affiliated Hospital of Xinjiang Medical University, No. 118 Henan West Road, Xinshi District, Urumqi, 830000, Xinjiang, China
| | - Yaling Zhang
- Department of Cardiology, The Fifth Affiliated Hospital of Xinjiang Medical University, No. 118 Henan West Road, Xinshi District, Urumqi, 830000, Xinjiang, China
| | - Shifeng Xing
- Department of Cardiology, The Fifth Affiliated Hospital of Xinjiang Medical University, No. 118 Henan West Road, Xinshi District, Urumqi, 830000, Xinjiang, China.
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10
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Roy S, Sheikh SZ, Furey TS. CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression. PLoS Comput Biol 2024; 20:e1012016. [PMID: 38630807 PMCID: PMC11057768 DOI: 10.1371/journal.pcbi.1012016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/29/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Network inference is used to model transcriptional, signaling, and metabolic interactions among genes, proteins, and metabolites that identify biological pathways influencing disease pathogenesis. Advances in machine learning (ML)-based inference models exhibit the predictive capabilities of capturing latent patterns in genomic data. Such models are emerging as an alternative to the statistical models identifying causative factors driving complex diseases. We present CoVar, an ML-based framework that builds upon the properties of existing inference models, to find the central genes driving perturbed gene expression across biological states. Unlike differentially expressed genes (DEGs) that capture changes in individual gene expression across conditions, CoVar focuses on identifying variational genes that undergo changes in their expression network interaction profiles, providing insights into changes in the regulatory dynamics, such as in disease pathogenesis. Subsequently, it finds core genes from among the nearest neighbors of these variational genes, which are central to the variational activity and influence the coordinated regulatory processes underlying the observed changes in gene expression. Through the analysis of simulated as well as yeast expression data perturbed by the deletion of the mitochondrial genome, we show that CoVar captures the intrinsic variationality and modularity in the expression data, identifying key driver genes not found through existing differential analysis methodologies.
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Affiliation(s)
- Satyaki Roy
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Shehzad Z. Sheikh
- Departments of Medicine and Genetics, Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Terrence S. Furey
- Departments of Genetics and Biology, Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, United States of America
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11
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Liang P, Wu Y, Qu S, Younis M, Wang W, Wu Z, Huang X. Exploring the biomarkers and potential therapeutic drugs for sepsis via integrated bioinformatic analysis. BMC Infect Dis 2024; 24:32. [PMID: 38166628 PMCID: PMC10763157 DOI: 10.1186/s12879-023-08883-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Sepsis is a life-threatening condition caused by an excessive inflammatory response to an infection, associated with high mortality. However, the regulatory mechanism of sepsis remains unclear. RESULTS In this study, bioinformatics analysis revealed the novel key biomarkers associated with sepsis and potential regulators. Three public datasets (GSE28750, GSE57065 and GSE95233) were employed to recognize the differentially expressed genes (DEGs). Taking the intersection of DEGs from these three datasets, GO and KEGG pathway enrichment analysis revealed 537 shared DEGs and their biological functions and pathways. These genes were mainly enriched in T cell activation, differentiation, lymphocyte differentiation, mononuclear cell differentiation, and regulation of T cell activation based on GO analysis. Further, pathway enrichment analysis revealed that these DEGs were significantly enriched in Th1, Th2 and Th17 cell differentiation. Additionally, five hub immune-related genes (CD3E, HLA-DRA, IL2RB, ITK and LAT) were identified from the protein-protein interaction network, and sepsis patients with higher expression of hub genes had a better prognosis. Besides, 14 drugs targeting these five hub related genes were revealed on the basis of the DrugBank database, which proved advantageous for treating immune-related diseases. CONCLUSIONS These results strengthen the new understanding of sepsis development and provide a fresh perspective into discriminating the candidate biomarkers for predicting sepsis as well as identifying new drugs for treating sepsis.
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Affiliation(s)
- Pingping Liang
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China
| | - Yongjian Wu
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China
| | - Siying Qu
- Department of Clinical Laboratory, Zhuhai Hospital of Integrated Traditional Chinese and Western Medicine, The Second People's Hospital of Zhuhai, Guangdong Province, Zhuhai, 519020, China
| | - Muhammad Younis
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China
| | - Wei Wang
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China
| | - Zhilong Wu
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China.
| | - Xi Huang
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China.
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China.
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12
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Mahmoudi A, Butler AE, De Vincentis A, Jamialahmadi T, Sahebkar A. Microarray-based Detection of Critical Overexpressed Genes in the Progression of Hepatic Fibrosis in Non-alcoholic Fatty Liver Disease: A Protein-protein Interaction Network Analysis. Curr Med Chem 2024; 31:3631-3652. [PMID: 37194229 DOI: 10.2174/0929867330666230516123028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/26/2023] [Accepted: 04/11/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is a prevalent cause of chronic liver disease and encompasses a broad spectrum of disorders, including simple steatosis, steatohepatitis, fibrosis, cirrhosis, and liver cancer. However, due to the global epidemic of NAFLD, where invasive liver biopsy is the gold standard for diagnosis, it is necessary to identify a more practical method for early NAFLD diagnosis with useful therapeutic targets; as such, molecular biomarkers could most readily serve these aims. To this end, we explored the hub genes and biological pathways in fibrosis progression in NAFLD patients. METHODS Raw data from microarray chips with GEO accession GSE49541 were downloaded from the Gene Expression Omnibus database, and the R package (Affy and Limma) was applied to investigate differentially expressed genes (DEGs) involved in the progress of low- (mild 0-1 fibrosis score) to high- (severe 3-4 fibrosis score) fibrosis stage NAFLD patients. Subsequently, significant DEGs with pathway enrichment were analyzed, including gene ontology (GO), KEGG and Wikipathway. In order to then explore critical genes, the protein-protein interaction network (PPI) was established and visualized using the STRING database, with further analysis undertaken using Cytoscape and Gephi software. Survival analysis was undertaken to determine the overall survival of the hub genes in the progression of NAFLD to hepatocellular carcinoma. RESULTS A total of 311 significant genes were identified, with an expression of 278 being upregulated and 33 downregulated in the high vs. low group. Gene functional enrichment analysis of these significant genes demonstrated major involvement in extracellular matrix (ECM)-receptor interaction, protein digestion and absorption, and the AGE-RAGE signaling pathway. The PPI network was constructed with 196 nodes and 572 edges with PPI enrichment using a p-value < 1.0 e-16. Based on this cut-off, we identified 12 genes with the highest score in four centralities: Degree, Betweenness, Closeness, and Eigenvector. Those twelve hub genes were CD34, THY1, CFTR, COL3A1, COL1A1, COL1A2, SPP1, THBS1, THBS2, LUM, VCAN, and VWF. Four of these hub genes, namely CD34, VWF, SPP1, and VCAN, showed significant association with the development of hepatocellular carcinoma. CONCLUSION This PPI network analysis of DEGs identified critical hub genes involved in the progression of fibrosis and the biological pathways through which they exert their effects in NAFLD patients. Those 12 genes offer an excellent opportunity for further focused research to determine potential targets for therapeutic applications.
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Affiliation(s)
- Ali Mahmoudi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Antonio De Vincentis
- Unit of Internal Medicine and Geriatrics, Università Campus Bio-Medico di Roma, Fondazione Policlinico Universitario Campus Bio-Medico di Roma, Via Alvaro del Portillo 200, Rome 00128, Italy
| | - Tannaz Jamialahmadi
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Medicine, The University of Western Australia, Perth, Australia
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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13
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Machuca-Sepúlveda J, Miranda J, Lefin N, Pedroso A, Beltrán JF, Farias JG. Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring. BIOLOGY 2023; 12:923. [PMID: 37508354 PMCID: PMC10376755 DOI: 10.3390/biology12070923] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/30/2023]
Abstract
Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.
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Affiliation(s)
- Jorge Machuca-Sepúlveda
- Doctoral Program on Natural Resources Sciences, Universidad de La Frontera, Avenida Francisco Salazar, 01145, P.O. Box 54-D, Temuco 4780000, Chile
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Javiera Miranda
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Nicolás Lefin
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Alejandro Pedroso
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Jorge F Beltrán
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Jorge G Farias
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
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14
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Zhang C, McIntosh KD, Sienkiewicz N, Stelzer EA, Graham JL, Lu J. Using cyanobacteria and other phytoplankton to assess trophic conditions: A qPCR-based, multi-year study in twelve large rivers across the United States. WATER RESEARCH 2023; 235:119679. [PMID: 37011576 PMCID: PMC10123349 DOI: 10.1016/j.watres.2023.119679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Phytoplankton is the essential primary producer in fresh surface water ecosystems. However, excessive phytoplankton growth due to eutrophication significantly threatens ecologic, economic, and public health. Therefore, phytoplankton identification and quantification are essential to understanding the productivity and health of freshwater ecosystems as well as the impacts of phytoplankton overgrowth (such as Cyanobacterial blooms) on public health. Microscopy is the gold standard for phytoplankton assessment but is time-consuming, has low throughput, and requires rich experience in phytoplankton morphology. Quantitative polymerase chain reaction (qPCR) is accurate and straightforward with high throughput. In addition, qPCR does not require expertise in phytoplankton morphology. Therefore, qPCR can be a useful alternative for molecular identification and enumeration of phytoplankton. Nonetheless, a comprehensive study is missing which evaluates and compares the feasibility of using qPCR and microscopy to assess phytoplankton in fresh water. This study 1) compared the performance of qPCR and microscopy in identifying and quantifying phytoplankton and 2) evaluated qPCR as a molecular tool to assess phytoplankton and indicate eutrophication. We assessed phytoplankton using both qPCR and microscopy in twelve large freshwater rivers across the United States from early summer to late fall in 2017, 2018, and 2019. qPCR- and microscope-based phytoplankton abundance had a significant positive linear correlation (adjusted R2 = 0.836, p-value < 0.001). Phytoplankton abundance had limited temporal variation within each sampling season and over the three years studied. The sampling sites in the midcontinent rivers had higher phytoplankton abundance than those in the eastern and western rivers. For instance, the concentration (geometric mean) of Bacillariophyta, Cyanobacteria, Chlorophyta, and Dinoflagellates at the sampling sites in the midcontinent rivers was approximately three times that at the sampling sites in the western rivers and approximately 18 times that at the sampling sites in the eastern rivers. Welch's analysis of variance indicates that phytoplankton abundance at the sampling sites in the midcontinent rivers was significantly higher than that at the sampling sites in the eastern rivers (p-value = 0.013) but was comparable to that at the sampling sites in the western rivers (p-value = 0.095). The higher phytoplankton abundance at the sampling sites in the midcontinent rivers was presumably because these rivers were more eutrophic. Indeed, low phytoplankton abundance occurred in oligotrophic or low trophic sites, whereas eutrophic sites had greater phytoplankton abundance. This study demonstrates that qPCR-based phytoplankton abundance can be a useful numerical indicator of the trophic conditions and water quality in freshwater rivers.
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Affiliation(s)
- Chiqian Zhang
- Department of Civil and Environmental Engineering, College of Sciences and Engineering, Southern University and A&M College, Baton Rouge, LA 70813, United States
| | - Kyle D McIntosh
- Oak Ridge Institute for Science and Education at the United States Environmental Protection Agency's Office of Research and Development, Oak Ridge, TN 37830, United States
| | - Nathan Sienkiewicz
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, United States
| | - Erin A Stelzer
- U.S. Geological Survey, Columbus, OH 43229, United States
| | | | - Jingrang Lu
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, United States.
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15
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Ahmed F, Samantasinghar A, Manzoor Soomro A, Kim S, Hyun Choi K. A systematic review of computational approaches to understand cancer biology for informed drug repurposing. J Biomed Inform 2023; 142:104373. [PMID: 37120047 DOI: 10.1016/j.jbi.2023.104373] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023]
Abstract
Cancer is the second leading cause of death globally, trailing only heart disease. In the United States alone, 1.9 million new cancer cases and 609,360 deaths were recorded for 2022. Unfortunately, the success rate for new cancer drug development remains less than 10%, making the disease particularly challenging. This low success rate is largely attributed to the complex and poorly understood nature of cancer etiology. Therefore, it is critical to find alternative approaches to understanding cancer biology and developing effective treatments. One such approach is drug repurposing, which offers a shorter drug development timeline and lower costs while increasing the likelihood of success. In this review, we provide a comprehensive analysis of computational approaches for understanding cancer biology, including systems biology, multi-omics, and pathway analysis. Additionally, we examine the use of these methods for drug repurposing in cancer, including the databases and tools that are used for cancer research. Finally, we present case studies of drug repurposing, discussing their limitations and offering recommendations for future research in this area.
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Affiliation(s)
- Faheem Ahmed
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea
| | | | | | - Sejong Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
| | - Kyung Hyun Choi
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea.
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16
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Liu J, Hu X, Hu Y, Chen P, Xu H, Hu W, Zhao Y, Wu P, Liu GL. Dual AuNPs detecting probe enhanced the NanoSPR effect for the high-throughput detection of the cancer microRNA21 biomarker. Biosens Bioelectron 2023; 225:115084. [PMID: 36693286 DOI: 10.1016/j.bios.2023.115084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/18/2022] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
The microRNA21 (miR-21), a specific tumor biomarker, is crucial for the diagnosis of several cancer types, and investigation of its overexpression pattern is important for cancer diagnosis. Herein, we report a low-cost, rapid, ultrasensitive, and convenient biosensing strategy for the detection of miR-21 using a nanoplasmonic array chip coupled with gold nanoparticles (AuNPs). This sensing platform combines the surface plasmon resonance effect of nanoplasmonics (NanoSPR) and the localized surface plasmon resonance (LSPR) effect, which allows the real-time monitoring of the subtle optical density (OD) changes caused by the variations in the dielectric constant in the process of the hybridization of the target miRNA. Using this method, the miRNA achieves a broad detection range from 100 aM to 1 μM, and with a limit of detection (LoD) of 1.85 aM. Furthermore, this assay also has a single-base resolution to discriminate the highly homologous miRNAs. More importantly, this platform has high throughput characteristics (96 samples can be detected simultaneously). This strategy exhibits more than 86.5 times enhancement in terms of sensitivity compared to that of traditional biosensors.
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Affiliation(s)
- Juxiang Liu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luo Yu Road, Wuhan, 430074, China
| | - Xulong Hu
- Institute of Geophysics and Geomatics, China University of Geosciences, Wuhan, 430074, China
| | - Yinxia Hu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ping Chen
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luo Yu Road, Wuhan, 430074, China
| | - Hao Xu
- Liangzhun (Shanghai) Industrial Co. Ltd., Shanghai, 200336, China
| | - Wenjun Hu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luo Yu Road, Wuhan, 430074, China
| | - Yanteng Zhao
- Department of Blood Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Ping Wu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luo Yu Road, Wuhan, 430074, China; School of Pharmacy, Wenzhou Medical University, Wenzhou, 325035, China; Research Units of Clinical Translation of Cell Growth Factors and Diseases Research, Chinese Academy of Medical Science, Wenzhou, 325035, China.
| | - Gang L Liu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luo Yu Road, Wuhan, 430074, China.
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17
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Zhou C, Zhu D, Zhou S, Wang H, Huang M. Screening differential circular RNA expression profiles and the potential role of hsa_circ_0085465 in liver cancer. J Cancer Res Ther 2023; 19:548-555. [PMID: 37470573 DOI: 10.4103/jcrt.jcrt_1868_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Aims This study aimed to screen the circular RNAs (circRNAs) that are differentially expressed between liver cancer and paired paracarcinoma tissues and then elucidate their role in cancer progression. Materials and Methods High-throughput sequencing of cancer and paired paracarcinoma tissues was followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of the parental genes of the differentially expressed circRNAs, which were also verified via real-time quantitative polymerase chain reaction analysis of the tissues. In addition, the function of selected circRNAs was determined using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4- sulfophenyl)-2H-tetrazolium (MTS) and transwell assays. Results Total 218 and 121 circRNAs were differentially upregulated and downregulated, respectively; these were mainly enriched with GO and KEGG terms related to biological functions. From five representatives of the differentially expressed circRNAs, we selected hsa_circ_0085465 for further analysis, discovering that its overexpression promoted the proliferation, migration, and invasion of 97 L cells. Conclusion Taken together, our results suggest that hsa_circ_0085465 is relevant to liver cancer progression.
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Affiliation(s)
- Churen Zhou
- Department of Interventional Radiology Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Duo Zhu
- Department of Interventional Radiology Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sibin Zhou
- Department of Interventional Radiology Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haofan Wang
- Department of Interventional Radiology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mingsheng Huang
- Department of Interventional Radiology Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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18
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He S, Lim GE. The Application of High-Throughput Approaches in Identifying Novel Therapeutic Targets and Agents to Treat Diabetes. Adv Biol (Weinh) 2023; 7:e2200151. [PMID: 36398493 DOI: 10.1002/adbi.202200151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/04/2022] [Indexed: 11/19/2022]
Abstract
During the past decades, unprecedented progress in technologies has revolutionized traditional research methodologies. Among these, advances in high-throughput drug screening approaches have permitted the rapid identification of potential therapeutic agents from drug libraries that contain thousands or millions of molecules. Moreover, high-throughput-based therapeutic target discovery strategies can comprehensively interrogate relationships between biomolecules (e.g., gene, RNA, and protein) and diseases and significantly increase the authors' knowledge of disease mechanisms. Diabetes is a chronic disease primarily characterized by the incapacity of the body to maintain normoglycemia. The prevalence of diabetes in modern society has become a severe public health issue that threatens the well-being of millions of patients. Although a number of pharmacological treatments are available, there is no permanent cure for diabetes, and discovering novel therapeutic targets and agents continues to be an urgent need. The present review discusses the technical details of high-throughput screening approaches in drug discovery, followed by introducing the applications of such approaches to diabetes research. This review aims to provide an example of the applicability of high-throughput technologies in facilitating different aspects of disease research.
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Affiliation(s)
- Siyi He
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
| | - Gareth E Lim
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
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Roy S, Sheikh SZ, Furey TS. CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523808. [PMID: 36712050 PMCID: PMC9882103 DOI: 10.1101/2023.01.12.523808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Network inference is used to model transcriptional, signaling, and metabolic interactions among genes, proteins, and metabolites that identify biological pathways influencing disease pathogenesis. Advances in machine learning (ML)-based inference models exhibit the predictive capabilities of capturing latent patterns in genomic data. Such models are emerging as an alternative to the statistical models identifying causative factors driving complex diseases. We present CoVar, an inference framework that builds upon the properties of existing inference models, to find the central genes driving perturbed gene expression across biological states. We leverage ML-based network inference to find networks that capture the strength of regulatory interactions. Our model first pinpoints a subset of genes, termed variational, whose expression variabilities typify the differences in network connectivity between the control and perturbed data. Variational genes, by being differentially expressed themselves or possessing differentially expressed neighbor genes, capture gene expression variability. CoVar then creates subnetworks comprising variational genes and their strongly connected neighbor genes and identifies core genes central to these subnetworks that influence the bulk of the variational activity. Through the analysis of yeast expression data perturbed by the deletion of the mitochondrial genome, we show that CoVar identifies key genes not found through independent differential expression analysis.
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20
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Tantray I, Ojha R, Sharma AP. Non-coding RNA and autophagy: Finding novel ways to improve the diagnostic management of bladder cancer. Front Genet 2023; 13:1051762. [PMID: 36685879 PMCID: PMC9845264 DOI: 10.3389/fgene.2022.1051762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
Major fraction of the human genome is transcribed in to the RNA but is not translated in to any specific functional protein. These transcribed but not translated RNA molecules are called as non-coding RNA (ncRNA). There are thousands of different non-coding RNAs present inside the cells, each regulating different cellular pathway/pathways. Over the last few decades non-coding RNAs have been found to be involved in various diseases including cancer. Non-coding RNAs are reported to function both as tumor enhancer and/or tumor suppressor in almost each type of cancer. Urothelial carcinoma of the urinary bladder is the second most common urogenital malignancy in the world. Over the last few decades, non-coding RNAs were demonstrated to be linked with bladder cancer progression by modulating different signalling pathways and cellular processes such as autophagy, metastasis, drug resistance and tumor proliferation. Due to the heterogeneity of bladder cancer cells more in-depth molecular characterization is needed to identify new diagnostic and treatment options. This review emphasizes the current findings on non-coding RNAs and their relationship with various oncological processes such as autophagy, and their applicability to the pathophysiology of bladder cancer. This may offer an understanding of evolving non-coding RNA-targeted diagnostic tools and new therapeutic approaches for bladder cancer management in the future.
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Affiliation(s)
- Ishaq Tantray
- School of Medicine, Department of Pathology, Stanford University, Stanford, CA, United States
| | - Rani Ojha
- Department of Urology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India,*Correspondence: Rani Ojha, ; Aditya P. Sharma,
| | - Aditya P. Sharma
- Department of Urology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India,*Correspondence: Rani Ojha, ; Aditya P. Sharma,
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21
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Smits N, Faulkner GJ. Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications. Methods Mol Biol 2023; 2607:151-171. [PMID: 36449163 DOI: 10.1007/978-1-0716-2883-6_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Over the past 20 years, high-throughput genomic assays have fundamentally changed how transposable elements (TEs) are studied. While short-read DNA sequencing has been at the heart of these efforts, novel technologies that generate longer reads are driving a shift in the field. Long-read sequencing now permits locus-specific approaches to locate individual TE insertions and understand their epigenetic and transcriptional regulation, while still profiling TE activity genome-wide. Here we provide detailed guidelines to implement Oxford Nanopore Technologies (ONT) sequencing to identify polymorphic TE insertions and profile TE epigenetic landscapes. Using human long interspersed element-1 (LINE-1, L1) as an example, we explain the procedures involved, including final visualization, and potential bottlenecks and pitfalls. ONT sequencing will be, in our view, a workhorse technology for the foreseeable future in the TE field.
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Affiliation(s)
- Nathan Smits
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia.
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia.
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22
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Chou L, Chang Y, Lan K, Liu M, Lu Y, Li X, Li P, Xu Y. CCK regulates osteogenic differentiation through TNFα/NF-κB in peri-implantitis. J Int Med Res 2022; 50:3000605221141312. [PMID: 36495169 DOI: 10.1177/03000605221141312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE Peri-implantitis is characterized by peri-implant mucositis and alveolar bone resorption. This study investigated cholecystokinin (CCK) expression and the mechanism underlying its involvement in peri-implantitis. METHODS mRNA sequencing was performed using the Gene Expression Omnibus database GSE106090. Human bone marrow mesenchymal stem cells (hBMSCs) were pretreated with various concentrations of CCK (0, 10, 30, or 100 nM) for 1 hour before induction in osteogenic differentiation medium for 2 weeks. Alkaline phosphatase (ALP) activity was determined, and the cells were stained with alizarin red. The expression levels of TNFα and the osteogenic markers ALP, RUNX2, and OCN were measured using quantitative real-time PCR. TNFα, phosphorylated P65, and total P65 levels were determined by western blot. RESULTS Compared with healthy individuals, 262 and 215 genes were up- and down-regulated, respectively, in the periodontal tissues of patients with peri-implantitis. CCK expression was significantly upregulated in patients with peri-implantitis. CCK reduced ALP activity, osteogenic differentiation, and levels of the osteogenic markers ALP, RUNX2, and OCN. Moreover, CCK promoted levels of TNFα and phosphorylated P65, which is a marker of activation for the NF-κB inflammatory pathway. CONCLUSIONS CCK regulates osteogenic differentiation through the TNFα/NF-κB axis in peri-implantitis.
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Affiliation(s)
- LongHang Chou
- Department of Orthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangdong, Guangzhou, China
| | - YaTing Chang
- Department of Orthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangdong, Guangzhou, China
| | - KaiWen Lan
- Department of Prosthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangdong, Guangzhou, China
| | - Meng Liu
- Department of Orthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangdong, Guangzhou, China
| | - YuKun Lu
- Department of Orthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangdong, Guangzhou, China
| | - XiaoLei Li
- Department of Orthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangdong, Guangzhou, China
| | - PeiRu Li
- Department of Orthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangdong, Guangzhou, China
| | - Yue Xu
- Department of Orthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangdong, Guangzhou, China
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23
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Temporelli PL. Polygenic risk score and age: an extra help in the cardiovascular prevention of the young? Eur Heart J Suppl 2022; 24:I181-I185. [PMID: 36380786 PMCID: PMC9662707 DOI: 10.1093/eurheartjsupp/suac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
All major guidelines recommend assessing the risk of atherosclerotic cardiovascular disease (ASCVD) using risk scores. In fact, it has been shown that their use at the population level increases the accuracy of event prediction and facilitates the choice of strategies to be adopted in primary prevention. In fact, their use in clinical practice is far from optimal and their predictive ability on an individual level is not excellent. Our genetic heritage is substantially stable from birth and determines a ‘baseline risk’ on which external influences act. Genetic information therefore has the potential to be an early predictor of risk. Common diseases such as diabetes mellitus, ASCVD and neurodegenerative diseases are conditioned by different genetic variants with small individual effects, so that a reliable risk prediction requires careful examination of the aggregate impact of these multiple variants. The polygenic risk score (PRS) is a tool that potentially enables this complex assessment and provides a new opportunity to explore our risk of developing common diseases, including coronary artery disease (CAD). In the future, it is possible that a specific PRS could be used as an independent CAD screening tool, but this requires a detailed assessment of the practical implications, including the population to be investigated, and the consequent interventions that would then be offered.
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Affiliation(s)
- Pier Luigi Temporelli
- Division of Cardiac Rehabilitation, Maugeri Scientific Clinical Institutes, IRCCS , Gattico-Veruno , Italy
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24
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Takashima Y, Murata A, Iida K, Sugai A, Hagiwara M, Nakatani K. Method for Identifying Sequence Motifs in Pre-miRNAs for Small-Molecule Binding. ACS Chem Biol 2022; 17:2817-2827. [PMID: 36150699 PMCID: PMC9594041 DOI: 10.1021/acschembio.2c00452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Non-coding RNAs are emerging targets for drug development because they are involved in various cellular processes. However, there are a few reliable design strategies for small molecules that can target RNAs. This paper reports a simple and efficient method to comprehensively analyze RNA motifs that can be bound by a specific small molecule. The method involves Dicer-mediated pre-miRNA cleavage and subsequent analysis of the reaction products by high-throughput sequencing. A pre-miRNA mutant library containing a randomized region at the Dicer cleavage site was used as the substrate for the reaction. Sequencing analysis of the products of the reaction carried out in the presence or absence of a synthetic small molecule identified the pre-miRNA mutants whose Dicer-mediated cleavage was significantly altered by the addition of the small molecule. The binding of the small molecule to the identified pre-miRNA mutants was confirmed by surface plasmon resonance, demonstrating the feasibility of our method.
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Affiliation(s)
- Yusuke Takashima
- Department
of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific
and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Asako Murata
- Department
of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific
and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan,
| | - Kei Iida
- Medical
Research Support Center, Kyoto University
Graduate School of Medicine, Konoecho Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ayako Sugai
- Department
of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific
and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Masatoshi Hagiwara
- Department
of Anatomy and Developmental Biology, Kyoto
University Graduate School of Medicine, Konoecho Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhiko Nakatani
- Department
of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific
and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan,
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25
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Srivastava N, Sarethy IP, Jeevanandam J, Danquah M. Emerging strategies for microbial screening of novel chemotherapeutics. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Zhu GD, Xie LM, Su JW, Cao XJ, Yin X, Li YP, Gao YM, Guo XG. Identification of differentially expressed genes and signaling pathways with Candida infection by bioinformatics analysis. Eur J Med Res 2022; 27:43. [PMID: 35314002 PMCID: PMC8935812 DOI: 10.1186/s40001-022-00651-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Opportunistic Candida species causes severe infections when the human immune system is weakened, leading to high mortality. METHODS In our study, bioinformatics analysis was used to study the high-throughput sequencing data of samples infected with four kinds of Candida species. And the hub genes were obtained by statistical analysis. RESULTS A total of 547, 422, 415 and 405 differentially expressed genes (DEGs) of Candida albicans, Candida glabrata, Candida parapsilosis and Candida tropicalis groups were obtained, respectively. A total of 216 DEGs were obtained after taking intersections of DEGs from the four groups. A protein-protein interaction (PPI) network was established using these 216 genes. The top 10 hub genes (FOSB, EGR1, JUNB, ATF3, EGR2, NR4A1, NR4A2, DUSP1, BTG2, and EGR3) were acquired through calculation by the cytoHubba plug-in in Cytoscape software. Validated by the sequencing data of peripheral blood, JUNB, ATF3 and EGR2 genes were significant statistical significance. CONCLUSIONS In conclusion, our study demonstrated the potential pathogenic genes in Candida species and their underlying mechanisms by bioinformatic analysis methods. Further, after statistical validation, JUNB, ATF3 and EGR2 genes were attained, which may be used as potential biomarkers with Candida species infection.
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Affiliation(s)
- Guo-Dong Zhu
- Department of Oncology, Guangzhou Geriatric Hospital, Guangzhou, 510180, China
| | - Li-Min Xie
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Jian-Wen Su
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xun-Jie Cao
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xin Yin
- Department of Pediatrics, The Pediatrics School of Guangzhou Medical University, Guangzhou, 510182, China
| | - Ya-Ping Li
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Yuan-Mei Gao
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China. .,Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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27
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Bacterial community identification in poultry carcasses using high-throughput next generation sequencing. Int J Food Microbiol 2022; 364:109533. [DOI: 10.1016/j.ijfoodmicro.2022.109533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/24/2022]
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28
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Zhou J, Xiong R, Zhou J, Guan X, Jiang G, Chen Y, Yang Q. Involvement of m6A regulatory factor IGF2BP1 in malignant transformation of human bronchial epithelial Beas-2B cells induced by tobacco carcinogen NNK. Toxicol Appl Pharmacol 2022; 436:115849. [PMID: 34974052 DOI: 10.1016/j.taap.2021.115849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/20/2021] [Accepted: 12/22/2021] [Indexed: 10/19/2022]
Abstract
Nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is a Group 1 human carcinogen, as classified by the International Agency for Research of Cancer (IARC), and plays a significant role in lung carcinogenesis. However, its carcinogenic mechanism has not yet been fully elucidated. In this study, we performed colony formation assays, soft-agar assays, and tumor growth in nude mice to show that 100 mg/L NNK facilitates the malignant transformation of human bronchial epithelial Beas-2B cells. Transcriptome sequencing showed that insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), a post-transcriptional regulator, was differentially expressed in NNK-induced malignant transformed Beas-2B cells (2B-NNK cells). Small interfering RNA (SiRNA) was used to downregulate the expression of the IGF2BP1 gene. The reduction in protein expression, cell proliferation rate, and colony-forming ability and the increase in the apoptosis rate of Beas-2B cells transfected with the SiRNA indicated a role for IGF2BP1 in NNK-induced malignant transformation. IGF2BP1 is an N6-methyladenosine (m6A) regulatory factor, but it is not known whether its association with m6A mediates the malignant transformation of cells. Therefore, we measured the overall levels of m6A in Beas-2B cells. We found that the overall m6A level was lower in 2B-NNK cells, and knocking down IGF2BP1, the overall level of m6A was restored. Hence, we concluded that IGF2BP1 is involved in the NNK-induced malignant transformation of Beas-2B cells, possibly via m6A modification. This study therefore contributes novel insights into the environmental pathogenesis of lung cancer and the gene regulatory mechanisms of chemical carcinogenesis.
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Affiliation(s)
- Jiaxin Zhou
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Rui Xiong
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Jiazhen Zhou
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Xinchao Guan
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Guanqing Jiang
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Yuyang Chen
- School of Anesthesiology, Southern Medical University, 1023-1063 Shatai Nan Road, Baiyun District, Guangzhou 510515, China
| | - Qiaoyuan Yang
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China; State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, No. 151 Yanjiang Road, Yuexiu District, Guangzhou 510120, China.
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29
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Bhargava K, Nath G, Bhargava A, Aseri GK, Jain N. Phage therapeutics: from promises to practices and prospectives. Appl Microbiol Biotechnol 2021; 105:9047-9067. [PMID: 34821965 PMCID: PMC8852341 DOI: 10.1007/s00253-021-11695-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 01/09/2023]
Abstract
The rise in multi-drug resistant bacteria and the inability to develop novel antibacterial agents limits our arsenal against infectious diseases. Antibiotic resistance is a global issue requiring an immediate solution, including the development of new antibiotic molecules and other alternative modes of therapy. This article highlights the mechanism of bacteriophage treatment that makes it a real solution for multidrug-resistant infectious diseases. Several case reports identified phage therapy as a potential solution to the emerging challenge of multi-drug resistance. Bacteriophages, unlike antibiotics, have special features, such as host specificity and do not impact other commensals. A new outlook has also arisen with recent advancements in the understanding of phage immunobiology, where phages are repurposed against both bacterial and viral infections. Thus, the potential possibility of phages in COVID-19 patients with secondary bacterial infections has been briefly elucidated. However, significant obstacles that need to be addressed are to design better clinical studies that may contribute to the widespread use of bacteriophage therapy against multi-drug resistant pathogens. In conclusion, antibacterial agents can be used with bacteriophages, i.e. bacteriophage-antibiotic combination therapy, or they can be administered alone in cases when antibiotics are ineffective.Key points• AMR, a consequence of antibiotic generated menace globally, has led to the resurgence of phage therapy as an effective and sustainable solution without any side effects and high specificity against refractory MDR bacterial infections.• Bacteriophages have fewer adverse reactions and can thus be used as monotherapy as well as in conjunction with antibiotics.• In the context of the COVID-19 pandemic, phage therapy may be a viable option.
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Affiliation(s)
- Kanika Bhargava
- Amity Institute of Microbial Technology, Amity University Rajasthan, Jaipur, 303 002 India
- Department of Microbiology, IMS, Banaras Hindu University, Varanasi, 221005 India
| | - Gopal Nath
- Department of Microbiology, IMS, Banaras Hindu University, Varanasi, 221005 India
| | - Amit Bhargava
- Department of Medicine, Hayes Memorial Hospital, SHUATS, Allahabad, 211007 India
| | - G. K. Aseri
- Amity Institute of Microbial Technology, Amity University Rajasthan, Jaipur, 303 002 India
| | - Neelam Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 303 002 India
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30
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Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches. DIVERSITY 2021. [DOI: 10.3390/d13090437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type, plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable.
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31
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Lambert M, Benmoussa A, Diallo I, Ouellet-Boutin K, Dorval V, Majeau N, Joly-Beauparlant C, Droit A, Bergeron A, Têtu B, Fradet Y, Pouliot F, Provost P. Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA. Int J Mol Sci 2021; 22:9757. [PMID: 34575920 PMCID: PMC8467515 DOI: 10.3390/ijms22189757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/02/2021] [Accepted: 09/05/2021] [Indexed: 12/17/2022] Open
Abstract
Using a modified RNA-sequencing (RNA-seq) approach, we discovered a new family of unusually short RNAs mapping to ribosomal RNA 5.8S, which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. Using a new quantitative detection method that we developed, we confirmed our RNA-seq data and determined that the minimal core doRNA sequence and its 13-nt variant C-doRNA (doRNA with a 5' Cytosine) are the two most abundant doRNAs, which, together, may outnumber microRNAs. The C-doRNA/doRNA ratio is stable within species but differed between species. doRNA and C-doRNA are mainly cytoplasmic and interact with heterogeneous nuclear ribonucleoproteins (hnRNP) A0, A1 and A2B1, but not Argonaute 2. Reporter gene activity assays suggest that C-doRNA may function as a regulator of Annexin II receptor (AXIIR) expression. doRNAs are differentially expressed in prostate cancer cells/tissues and may control cell migration. These findings suggest that unusually short RNAs may be more abundant and important than previously thought.
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Affiliation(s)
- Marine Lambert
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Abderrahim Benmoussa
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Idrissa Diallo
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Katheryn Ouellet-Boutin
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Véronique Dorval
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
| | - Nathalie Majeau
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
| | - Charles Joly-Beauparlant
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Molecular Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada
| | - Arnaud Droit
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Molecular Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada
| | - Alain Bergeron
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Bernard Têtu
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Yves Fradet
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Frédéric Pouliot
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Patrick Provost
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
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Chen S, Ren C, Zhai J, Yu J, Zhao X, Li Z, Zhang T, Ma W, Han Z, Ma C. CAFU: a Galaxy framework for exploring unmapped RNA-Seq data. Brief Bioinform 2021; 21:676-686. [PMID: 30815667 PMCID: PMC7299299 DOI: 10.1093/bib/bbz018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/23/2019] [Accepted: 01/27/2019] [Indexed: 12/13/2022] Open
Abstract
A widely used approach in transcriptome analysis is the alignment of short reads to a reference genome. However, owing to the deficiencies of specially designed analytical systems, short reads unmapped to the genome sequence are usually ignored, resulting in the loss of significant biological information and insights. To fill this gap, we present Comprehensive Assembly and Functional annotation of Unmapped RNA-Seq data (CAFU), a Galaxy-based framework that can facilitate the large-scale analysis of unmapped RNA sequencing (RNA-Seq) reads from single- and mixed-species samples. By taking advantage of machine learning techniques, CAFU addresses the issue of accurately identifying the species origin of transcripts assembled using unmapped reads from mixed-species samples. CAFU also represents an innovation in that it provides a comprehensive collection of functions required for transcript confidence evaluation, coding potential calculation, sequence and expression characterization and function annotation. These functions and their dependencies have been integrated into a Galaxy framework that provides access to CAFU via a user-friendly interface, dramatically simplifying complex exploration tasks involving unmapped RNA-Seq reads. CAFU has been validated with RNA-Seq data sets from wheat and Zea mays (maize) samples. CAFU is freely available via GitHub: https://github.com/cma2015/CAFU.
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Affiliation(s)
- Siyuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Chengzhi Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Jingjing Zhai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Jiantao Yu
- College of Information Engineering, Northwest Agriculture and Forestry University
| | - Xuyang Zhao
- College of Information Engineering, Northwest Agriculture and Forestry University
| | - Zelong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Ting Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Wenlong Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Zhaoxue Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
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33
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Doaré E, Héry-Arnaud G, Devauchelle-Pensec V, Alegria GC. Healthy Patients Are Not the Best Controls for Microbiome-Based Clinical Studies: Example of Sjögren's Syndrome in a Systematic Review. Front Immunol 2021; 12:699011. [PMID: 34394092 PMCID: PMC8358393 DOI: 10.3389/fimmu.2021.699011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/13/2021] [Indexed: 01/03/2023] Open
Abstract
Introduction It has been hypothesized that gut and oral dysbiosis may contribute to the development of primary Sjögren's syndrome (pSS). The aim of this systematic review was to assemble available data regarding the oral and gut microbiota in pSS and to compare them to data from healthy individuals and patients with dry symptoms without a diagnosis of Sjögren's syndrome or lupus disease to identify dysbiosis and discuss the results. Methodology Using the PRISMA guidelines, we systematically reviewed studies that compared the oral and gut microbiota of Sjögren's patients and controls. The PubMed database and Google Scholar were searched. Results Two-hundred and eighty-nine studies were found, and 18 studies were included: 13 referred to the oral microbiota, 4 referred to the gut microbiota, and 1 referred to both anatomical sites. The most frequent controls were healthy volunteers and patients with sicca symptoms. The most common analysis method used was 16S-targeted metagenomics. The results were mostly heterogeneous, and the results regarding diversity were not always in accordance. Dysbiosis in pSS was not confirmed, and reduced salivary secretion seems to explain more microbial changes than the underlying disease. Conclusion These heterogeneous results might be explained by the lack of a standardized methodology at each step of the process and highlight the need for guidelines. Our review provides evidence that sicca patients seem to be more relevant than healthy subjects as a control group.
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Affiliation(s)
- Elise Doaré
- Rheumatology Department, Reference Centre of Rare Autoimmune Diseases, Cavale Blanche Hospital and Brest University, INSERM UMR 1227, Brest, France
| | - Geneviève Héry-Arnaud
- UMR1078, Génétique, Génomique Fonctionnelle Et Biotechnologies, INSERM, Université de Brest, EFS, IBSAM, Brest, France.,Centre Brestois d'Analyse du Microbiote, Hôpital La Cavale Blanche, CHRU de Brest, Brest, France
| | - Valérie Devauchelle-Pensec
- Rheumatology Department, Reference Centre of Rare Autoimmune Diseases, Cavale Blanche Hospital and Brest University, INSERM UMR 1227, Brest, France
| | - Guillermo Carvajal Alegria
- Rheumatology Department, Reference Centre of Rare Autoimmune Diseases, Cavale Blanche Hospital and Brest University, INSERM UMR 1227, Brest, France
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Lu J, Ma X, Gao WC, Zhang X, Fu Y, Liu Q, Tian L, Qin XD, Yang W, Zheng HY, Zheng CB. Gastrodin Exerts Cardioprotective Action via Inhibition of Insulin-Like Growth Factor Type 2/Insulin-Like Growth Factor Type 2 Receptor Expression in Cardiac Hypertrophy. ACS OMEGA 2021; 6:16763-16774. [PMID: 34250336 PMCID: PMC8264851 DOI: 10.1021/acsomega.1c00797] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/10/2021] [Indexed: 05/05/2023]
Abstract
Pathological cardiac hypertrophy is commonly associated with an upregulation of fetal genes, fibrosis, cardiac dysfunction, and heart failure. Previous studies have demonstrated that gastrodin (GAS) exerts cardioprotective action in the treatment of cardiac hypertrophy. However, the mechanism by which GAS protects against cardiac hypertrophy is yet to be elucidated. A mouse model of myocardial hypertrophy was established using an angiotensin II (Ang II) induction. GAS (5 or 50 mg/kg/d) was orally administered every day starting 7 days prior to the Ang II infusion combined with sham-operated controls. Heart samples from each group were collected for RNA sequencing. Using bioinformatics analysis, the key differentially expressed genes (DEGs) that are involved in reversing cardiac function were identified. Through bioinformatics analysis, the key DEGs that are involved in GAS's inhibition of Ang II-induced abnormal gene expression within the heart were identified. This was further validated using quantitative real-time PCR and Western blotting in neonatal rat cardiomyocytes (NRCMs). Oral administration of GAS significantly suppressed the Ang II-induced increase in heart size and heart weight to body weight. Furthermore, pretreatment of the NRCMs with GAS led to a dose-dependent inhibition of Ang II-induced increases in Nppb mRNA expression. We identified 620 upregulated and 87 downregulated Ang II-induced DEGs II, among which the expression patterns of 58 and 146 genes were inverted by low-dose and high-dose GAS, respectively. These inverted DEGs were found to be mainly enriched in the biological processes of regulation of Ras protein signal transduction, heart contraction, covalent chromatin modification, glucose metabolism, and positive regulation of cell cycle. Among them, the insulin-like growth factor type 2 (Igf2) gene, which was found to be highly reversed and downregulated by GAS, served as a core gene linking energy metabolism, immune regulation, and systemic development. Subsequent functional verification demonstrated that IGF2, and its receptor IGF2R, is one of the targets of GAS that helps protect against cardiac hypertrophy. Taken together, we have identified, for the first time, IGF2/IGF2R as a potential target influenced by GAS in the prevention of cardiac hypertrophy.
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Affiliation(s)
- Jun Lu
- Department
of Pharmacology, Guilin Medical University, Guilin 541199, China
| | - Xin Ma
- School
of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology
for Natural Products, Kunming Medical University, Kunming 650500, China
- Key
Laboratory of Animal Models and Human Diseases Mechanisms of Chinese
Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen-Cong Gao
- School
of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology
for Natural Products, Kunming Medical University, Kunming 650500, China
- Key
Laboratory of Animal Models and Human Diseases Mechanisms of Chinese
Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xin Zhang
- School
of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology
for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Yuanling Fu
- School
of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology
for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Qian Liu
- School
of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology
for Natural Products, Kunming Medical University, Kunming 650500, China
- Key
Laboratory of Animal Models and Human Diseases Mechanisms of Chinese
Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Lixiang Tian
- School
of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology
for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Xiao-Dan Qin
- Department
of Pharmacology, Guilin Medical University, Guilin 541199, China
| | - Weimin Yang
- School
of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology
for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Hong-Yi Zheng
- Key
Laboratory of Animal Models and Human Diseases Mechanisms of Chinese
Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chang-Bo Zheng
- School
of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology
for Natural Products, Kunming Medical University, Kunming 650500, China
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35
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Muse ED, Chen SF, Torkamani A. Monogenic and Polygenic Models of Coronary Artery Disease. Curr Cardiol Rep 2021; 23:107. [PMID: 34196841 DOI: 10.1007/s11886-021-01540-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/17/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE OF THE REVIEW Coronary artery disease (CAD) is a common disease globally attributable to the interplay of complex genetic and lifestyle factors. Here, we review how genomic sequencing advances have broadened the fundamental understanding of the monogenic and polygenic contributions to CAD and how these insights can be utilized, in part by creating polygenic risk estimates, for improved disease risk stratification at the individual patient level. RECENT FINDINGS Initial studies linking premature CAD with rare familial cases of elevated blood lipids highlighted high-risk monogenic contributions, predominantly presenting as familial hypercholesterolemia (FH). More commonly CAD genetic risk is a function of multiple, higher frequency variants each imparting lower magnitude of risk, which can be combined to form polygenic risk scores (PRS) conveying significant risk to individuals at the extremes. However, gaps remain in clinical validation of PRSs, most notably in non-European populations. With improved and more broadly utilized genomic sequencing technologies, the genetic underpinnings of coronary artery disease are being unraveled. As a result, polygenic risk estimation is poised to become a widely used and powerful tool in the clinical setting. While the use of PRSs to augment current clinical risk stratification for optimization of cardiovascular disease risk by lifestyle change or therapeutic targeting is promising, we await adequately powered, prospective studies, demonstrating the clinical utility of polygenic risk estimation in practice.
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Affiliation(s)
- Evan D Muse
- Scripps Research Translational Institute, Scripps Research, 3344 N Torrey Pines Court, Suite 300, La Jolla, CA, 92037, USA.,Division of Cardiovascular Diseases, Scripps Clinic, La Jolla, CA, 92037, USA
| | - Shang-Fu Chen
- Scripps Research Translational Institute, Scripps Research, 3344 N Torrey Pines Court, Suite 300, La Jolla, CA, 92037, USA
| | - Ali Torkamani
- Scripps Research Translational Institute, Scripps Research, 3344 N Torrey Pines Court, Suite 300, La Jolla, CA, 92037, USA.
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36
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Jiang Z, Fa B, Zhang X, Wang J, Feng Y, Shi H, Zhang Y, Sun D, Wang H, Yin S. Identifying genetic risk variants associated with noise-induced hearing loss based on a novel strategy for evaluating individual susceptibility. Hear Res 2021; 407:108281. [PMID: 34157653 DOI: 10.1016/j.heares.2021.108281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 05/10/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND The overall genetic profile for noise-induced hearing loss (NIHL) remains elusive. Herein we proposed a novel machine learning (ML) based strategy to evaluate individual susceptibility to NIHL and identify the underlying genetic risk variants based on a subsample of participants with extreme phenotypes. METHODS Five features (age, sex, cumulative noise exposure [CNE], smoking, and alcohol drinking status) of 5,539 shipbuilding workers from large cross-sectional surveys were included in four ML classification models to predict their hearing levels. The area under the curve (AUC) and prediction accuracy were exploited to evaluate the performance of the models. Based on the prediction error of the ML models, the NIHL-susceptible group (n=150) and NIHL-resistant group (n=150) with a paradoxical relationship between hearing levels and features were separately screened, to identify the underlying variants associated with NIHL risk using whole-exome sequencing (WES). Subsequently, candidate risk variants were validated in an additional replication cohort (n=2108), followed by a meta-analysis. RESULTS With 10-fold cross-validation, the performances of the four ML models were robust and similar, with average AUCs and accuracies ranging from 0.783 to 0.798 and 73.7% to 73.8%, respectively. The phenotypes of the NIHL-susceptible and NIHL-resistant groups were significantly different (all p<0.001). After WES analysis and filtering, 12 risk variants contributing to NIHL susceptibility were identified and replicated. The meta-analyses showed that the A allele of CDH23 rs41281334 (odds ratio [OR]=1.506, 95% confidence interval [CI]=1.106-2.051) and the C allele of WHRN rs12339210 (OR=3.06, 95% CI=1.398-6.700) were significantly associated with increased risk of NIHL after adjustment for confounding factors. CONCLUSIONS This study revealed two genetic variants in CDH23 rs41281334 and WHRN rs12339210 that associated with NIHL risk, based on a promising approach for evaluating individual susceptibility using ML models.
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Affiliation(s)
- Zhuang Jiang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China; Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai 200233, China; Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai 200233, China
| | - Botao Fa
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xunmiao Zhang
- Department of Occupational Disease, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Jiping Wang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China; Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai 200233, China; Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai 200233, China
| | - Yanmei Feng
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China; Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai 200233, China; Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai 200233, China
| | - Haibo Shi
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China; Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai 200233, China; Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai 200233, China
| | - Yue Zhang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Daoyuan Sun
- Department of Occupational Disease, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.
| | - Hui Wang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China; Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai 200233, China; Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai 200233, China.
| | - Shankai Yin
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China; Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai 200233, China; Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai 200233, China
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37
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Hashemi S, Hashemi SE, Lien KM, Lamb JJ. Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production. Microorganisms 2021; 9:microorganisms9061162. [PMID: 34071282 PMCID: PMC8226781 DOI: 10.3390/microorganisms9061162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.
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Affiliation(s)
- Seyedbehnam Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Sayed Ebrahim Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Kristian M. Lien
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Jacob J. Lamb
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
- Department of Electronic Systems, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway
- Correspondence:
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38
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Southern A, El-Bahrawy M. Advances in understanding the molecular pathology of gynecological malignancies: the role and potential of RNA sequencing. Int J Gynecol Cancer 2021; 31:1159-1164. [PMID: 34016704 DOI: 10.1136/ijgc-2021-002509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 11/03/2022] Open
Abstract
For many years technological limitations restricted the progress of identifying the underlying genetic causes of gynecologicalcancers. However, during the past decade, high-throughput next-generation sequencing technologies have revolutionized cancer research. RNA sequencing has arisen as a very useful technique in expanding our understanding of genome changes in cancer. Cancer is characterized by the accumulation of genetic alterations affecting genes, including substitutions, insertions, deletions, translocations, gene fusions, and alternative splicing. If these aberrant genes become transcribed, aberrations can be detected by RNA sequencing, which will also provide information on the transcript abundance revealing the expression levels of the aberrant genes. RNA sequencing is considered the technique of choice when studying gene expression and identifying new RNA species. This is due to the quantitative and qualitative improvement that it has brought to transcriptome analysis, offering a resolution that allows research into different layers of transcriptome complexity. It has also been successful in identifying biomarkers, fusion genes, tumor suppressors, and uncovering new targets responsible for drug resistance in gynecological cancers. To illustrate that we here review the role of RNA sequencing in studies that enhanced our understanding of the molecular pathology of gynecological cancers.
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Affiliation(s)
- Alba Southern
- Surgery and Cancer, Imperial College London, London, UK
| | - Mona El-Bahrawy
- Metabolism, Digestion and Reproduction, Imperial College London, London, UK .,Pathology, Alexandria University Faculty of Medicine, Alexandria, Egypt
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39
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Westaway JAF, Huerlimann R, Miller CM, Kandasamy Y, Norton R, Rudd D. Methods for exploring the faecal microbiome of premature infants: a review. Matern Health Neonatol Perinatol 2021; 7:11. [PMID: 33685524 PMCID: PMC7941982 DOI: 10.1186/s40748-021-00131-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
The premature infant gut microbiome plays an important part in infant health and development, and recognition of the implications of microbial dysbiosis in premature infants has prompted significant research into these issues. The approaches to designing investigations into microbial populations are many and varied, each with its own benefits and limitations. The technique used can influence results, contributing to heterogeneity across studies. This review aimed to describe the most common techniques used in researching the preterm infant microbiome, detailing their various limitations. The objective was to provide those entering the field with a broad understanding of available methodologies, so that the likely effects of their use can be factored into literature interpretation and future study design. We found that although many techniques are used for characterising the premature infant microbiome, 16S rRNA short amplicon sequencing is the most common. 16S rRNA short amplicon sequencing has several benefits, including high accuracy, discoverability and high throughput capacity. However, this technique has limitations. Each stage of the protocol offers opportunities for the injection of bias. Bias can contribute to variability between studies using 16S rRNA high throughout sequencing. Thus, we recommend that the interpretation of previous results and future study design be given careful consideration.
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Affiliation(s)
- Jacob A F Westaway
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia.
| | - Roger Huerlimann
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
| | - Catherine M Miller
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia
| | - Yoga Kandasamy
- Townsville University Hospital, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Robert Norton
- Pathology Queensland, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Donna Rudd
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
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40
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Ren X, Liang S, Li Y, Ji Y, Li L, Qin C, Fang K. ENAM gene associated with T classification and inhibits proliferation in renal clear cell carcinoma. Aging (Albany NY) 2021; 13:7035-7051. [PMID: 33539322 PMCID: PMC7993715 DOI: 10.18632/aging.202558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/23/2020] [Indexed: 01/18/2023]
Abstract
The potential involvement of T classification-related genes in renal clear cell carcinoma (ccRCC) must be further explored. Public data were obtained from The Cancer Genome Atlas (TCGA) database. An overall survival (OS) predictive model was developed and validated (TCGA train, 5 years, AUC = 0.73, 3 years, AUC = 0.73, 1 year, AUC = 0.76; TCGA test, 5 years, AUC = 0.74, 3 years, AUC = 0.65, 1 year, AUC = 0.73; TCGA all, 5 years, AUC = 0.72, 3 years, AUC = 0.71, 1 year, AUC = 0.75). Finally, ENAM was selected for further analysis. In vitro experiment indicated that ENMA is downregulated in ccRCC, and its knockdown could promote proliferation in two cancer cell lines (OSRC-2 and SW839). Immune infiltration analysis revealed that ENAM could remarkably increase the content of cytotoxic cells, NK CD56 cells, NK cells and CD8+ T cells in the tumor immune microenvironment, which may be one reason for its tumor-inhibiting effect. In summary, ENAM may suppress cell proliferation in ccRCC and can be used as a potential reference value for the relief and immunotherapy of ccRCC.
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Affiliation(s)
- Xiaohan Ren
- The State Key Laboratory of Reproductive Medicine, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shengjie Liang
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Huinan, Pudong, Shanghai 201399, China
| | - Yang Li
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Huinan, Pudong, Shanghai 201399, China
| | - Yisheng Ji
- The First Clinical Medical College, Nanjing Medical University, Nanjing 211166, China
| | - Lin Li
- The First Clinical Medical College, Nanjing Medical University, Nanjing 211166, China
| | - Chao Qin
- The State Key Laboratory of Reproductive Medicine, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Kai Fang
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Huinan, Pudong, Shanghai 201399, China
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41
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Balasubramanian R, Pal S, Rao A, Naik A, Chakraborty B, Maiti PK, Varma MM. DNA Translocation through Vertically Stacked 2D Layers of Graphene and Hexagonal Boron Nitride Heterostructure Nanopore. ACS APPLIED BIO MATERIALS 2021; 4:451-461. [PMID: 35014296 DOI: 10.1021/acsabm.0c00929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cost-effective, fast, and reliable DNA sequencing can be enabled by advances in nanopore-based methods, such as the use of atomically thin graphene membranes. However, strong interaction of DNA bases with graphene leads to undesirable effects such as sticking of DNA strands to the membrane surface. While surface functionalization is one way to counter this problem, here, we present another solution based on a heterostructure nanopore system, consisting of a monolayer of graphene and hexagonal boron nitride (hBN) each. Molecular dynamics studies of DNA translocation through this heterostructure nanopore revealed a surprising and crucial influence of the heterostructure layer order in controlling the base specific signal variability. Specifically, the heterostructure with graphene on top of hBN had nearly 3-10× lower signal variability than the one with hBN on top of graphene. Simulations point to the role of differential underside sticking of DNA bases as a possible reason for the observed influence of the layer order. Our studies can guide the development of experimental systems to study and exploit DNA translocation through two-dimensional heterostructure nanopores for single molecule sequencing and sensing applications.
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Affiliation(s)
| | - Sohini Pal
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, United States
| | - Akshay Naik
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Manoj M Varma
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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42
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Zhuo DX, Ginder K, Hardin EA. Markers of Immune Function in Heart Transplantation: Implications for Immunosuppression and Screening for Rejection. Curr Heart Fail Rep 2021; 18:33-40. [PMID: 33400150 DOI: 10.1007/s11897-020-00499-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
PURPOSE OF REVIEW Recent developments in high-throughput DNA and RNA sequencing technologies have facilitated the development of noninvasive assays to monitor heart transplant rejection. In this review, we summarize existing assays employed for the surveillance of allograft rejection, as well as promising future directions for such tests in the molecular biology field. RECENT FINDINGS The AlloMap genome expression profiling assay remains the only noninvasive test for rejection surveillance and is incorporated into the International Society of Heart and Lung Transplantation guidelines. Other efforts have focused on messenger RNA (mRNA), microRNA (miRNA), and donor-derived cell-free DNA (dd-cfDNA) as potential viable biomarkers. Mitochondrial pathways in allograft necroptosis and inflammation signaling may represent a novel direction for future research endeavors. Although endomyocardial biopsy remains the gold standard, several converging areas of molecular biology could soon yield successful alternative methods of heart transplant rejection monitoring, with the distinct advantage of avoiding procedural complications.
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Affiliation(s)
- David X Zhuo
- Fellow, Advanced Heart Failure and Transplant Cardiology, Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9047, USA
| | - Katie Ginder
- Nurse Practitioner, Advanced Heart Failure, Transplant, LVAD, Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E Ashley Hardin
- Internal Medicine, Advanced Heart Failure and Transplant Cardiology, Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, 5959 Harry Hines Boulevard, Ste #HP.8.110, Dallas, TX, 75390-9047, USA.
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43
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Tahery N, Khodadost M, Jahani Sherafat S, Rezaei Tavirani M, Ahmadi N, Montazer F, Rezaei Tavirani M, Naderi N. C-reactive protein as a possible marker for severity and mortality of COVID-19 infection. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2021; 14:S118-S122. [PMID: 35154611 PMCID: PMC8817756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/29/2021] [Indexed: 11/24/2022]
Abstract
AIM The present study aimed to introduce a possible biomarker to differentiate between severe and fatal conditions of COVID-19. BACKGROUND The COVID-19 pandemic, appearing as a complicated health problem, has changed the lifestyle of people in recent years. Clinical findings indicate mild, severe, and fatal conditions of this disease. Prediction of disease severity is a significant point in managing COVID-19 infection. METHODS In this study, 195 differentially expressed genes (DEGs) that discriminate between fatal and severe conditions in patients were extracted from the literature and screened to determine the significant ones. The significant DEGs plus the 90 first neighbors added from the STRING database were included in the interactome using Cytoscape software v 3.7.2. The central nodes of the analyzed network were identified and assessed. RESULTS Ten significant DEGs were candidates for assessment, of which 9 were recognized by the STRING database. IL6, ALB, TNF, CRP, INS, MPO, C3, CXCL8, TTR, and TLR4 were determined as central nodes; IL6, CRP, and TTR were highlighted as the critical genes related to the severity of COVID-19 infection. CONCLUSION CRP was identified as the best possible biomarker with levels related to the severity and fatality of COVID-19 infection.
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Affiliation(s)
| | - Mahmood Khodadost
- School of Traditional Medicine Shahid, Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Jahani Sherafat
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nayebali Ahmadi
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Montazer
- Firoozabadi Clinical Research Development Unit, Iran University of Medical Sciences, Tehran, Iran
| | | | - Nosratollah Naderi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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44
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Nguyen NNT, McCarthy C, Lantigua D, Camci-Unal G. Development of Diagnostic Tests for Detection of SARS-CoV-2. Diagnostics (Basel) 2020; 10:E905. [PMID: 33167445 PMCID: PMC7694548 DOI: 10.3390/diagnostics10110905] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
One of the most effective ways to prevent the spread of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is to develop accurate and rapid diagnostic tests. There are a number of molecular, serological, and imaging methods that are used to diagnose this infection in hospitals and clinical settings. The purpose of this review paper is to present the available approaches for detecting SARS-CoV-2 and address the advantages and limitations of each detection method. This work includes studies from recent literature publications along with information from the manufacturer's manuals of commercially available SARS-CoV-2 diagnostic products. Furthermore, supplementary information from the Food & Drug Administration (FDA), Centers for Disease Control and Prevention (CDC), and World Health Organization (WHO) is cited. The viral components targeted for virus detection, the principles of each diagnostic technique, and the detection efficiency of each approach are discussed. The potential of using diagnostic tests that were originally developed for previous epidemic viruses is also presented.
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Affiliation(s)
- Ngan N. T. Nguyen
- Department of Chemical Engineering, University of Massachusetts Lowell, One University Avenue, Lowell, MA 01854, USA; (N.N.T.N.); (C.M.); (D.L.)
| | - Colleen McCarthy
- Department of Chemical Engineering, University of Massachusetts Lowell, One University Avenue, Lowell, MA 01854, USA; (N.N.T.N.); (C.M.); (D.L.)
| | - Darlin Lantigua
- Department of Chemical Engineering, University of Massachusetts Lowell, One University Avenue, Lowell, MA 01854, USA; (N.N.T.N.); (C.M.); (D.L.)
- Biomedical Engineering and Biotechnology Program, University of Massachusetts Lowell, One University Avenue, Lowell, MA 01854, USA
| | - Gulden Camci-Unal
- Department of Chemical Engineering, University of Massachusetts Lowell, One University Avenue, Lowell, MA 01854, USA; (N.N.T.N.); (C.M.); (D.L.)
- Department of Surgery, University of Massachusetts Medical School, 55 Lake Avenue, Worcester, MA 01655, USA
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45
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Figtree GA, Vernon ST, Nicholls SJ. Taking the next steps to implement polygenic risk scoring for improved risk stratification and primary prevention of coronary artery disease. Eur J Prev Cardiol 2020; 29:580-587. [DOI: 10.1093/eurjpc/zwaa030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/30/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022]
Abstract
Abstract
Coronary artery disease (CAD) remains the leading cause of death worldwide. The role of hypertension, cholesterol, diabetes mellitus, and smoking in driving disease has been well recognized at a population level and has been the target of primary prevention strategies for over 50 years with substantial impact. However, in many cases, these factors alone do not provide enough precision at the individual level to allow physicians and patients to take appropriate preventive measures and many patients continue to suffer acute coronary syndromes in the absence of these risk factors. Recent advances in user-friendly chip designs, high speed throughput, and economic efficiency of genome-wide association studies complemented by advances in statistical analytical approaches have facilitated the rapid development of polygenic risk scores (PRSs). The latest PRSs combine data regarding hundreds of thousands of single-nucleotide polymorphisms to predict chronic diseases including CAD. Novel CAD PRSs are strong predictors of risk and may have application, in a complementary manner with existing risk prediction algorithms. However, there remain substantial controversies, and ultimately, we need to move forward from observational studies to prospectively and rigorously assess the potential impact if widespread implementation is to be aspired to. Consideration needs to be made of ethnicity, sex, as well as age, and risk estimate based on existing non-genomic algorithms. We provide an overview and commentary on the important advances in deriving and validating PRSs, as well as pragmatic considerations that will be required for implementation of the new knowledge into clinical practice.
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Affiliation(s)
| | - Stephen Thomas Vernon
- Cardiothoracic and Vascular Health, Level 12, Kolling Institute of Medical Research, Northern Sydney Local Health District, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2050, Australia
| | - Stephen James Nicholls
- Monash Heart, 246 Clayton Road, Clayton, Victoria, 3168, Australia
- Monash Health, Monash University, Melbourne, Clayton, Victoria, 3800, Australia
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46
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Pisano MP, Grandi N, Tramontano E. High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development. Viruses 2020; 12:E633. [PMID: 32545287 PMCID: PMC7354619 DOI: 10.3390/v12060633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 01/19/2023] Open
Abstract
Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.
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Affiliation(s)
- Maria Paola Pisano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042 Cagliari, Italy
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47
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Yoon HY, Lee SY. An Assessment of the Bacterial Diversity found in Dental Unit Waterlines using the Illumina MiSeq. Biocontrol Sci 2020; 24:201-212. [PMID: 31875612 DOI: 10.4265/bio.24.201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Water from the waterlines of dental units is often contaminated with bacteria but there have been few studies accurately assessing the diversity of these bacterial populations. The aim of our study was to assess the bacterial diversity present in water collected from dental unit waterlines using the Illumina MiSeq. Water was collected from two separate dental units located in a dental hospital and two units found in two separate private clinics in Gangneung-si, Korea. From the four water samples that were analyzed, a total of 233 bacterial genera were identified. The most abundant genera were Sphingomonas (25%), Halomonas (20%), Reyranella (8%), and Novosphingobium (6%). Halomonas was more prevalent in the two dental units located at the dental hospital, while Reyranella and Sphingomonas were more commonly found in the private dental clinics. Only 19 of the 233 identified genera were common between water samples from all dental units. Opportunistic pathogens were shown to account for 7.7% of the total bacterial genera identified. Our results have demonstrated that there is a wide assortment of bacterial genera present in dental unit waterlines.
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Affiliation(s)
- Hye Young Yoon
- Department of Oral Microbiology, College of Dentistry, Research Institute of Oral Science, Gangneung-Wonju National University
| | - Si Young Lee
- Department of Oral Microbiology, College of Dentistry, Research Institute of Oral Science, Gangneung-Wonju National University
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48
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Chen LQ, Zhao WS, Luo GZ. Mapping and editing of nucleic acid modifications. Comput Struct Biotechnol J 2020; 18:661-667. [PMID: 32257049 PMCID: PMC7113611 DOI: 10.1016/j.csbj.2020.03.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/29/2020] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
Modification on nucleic acid plays a pivotal role in controlling gene expression. Various kinds of modifications greatly increase the information-encoding capacity of DNA and RNA by introducing extra chemical group to existing bases instead of altering the genetic sequences. As a marker on DNA or RNA, nucleic acid modification can be recognized by specific proteins, leading to versatile regulation of gene expression. However, modified and regular bases are often indistinguishable by most conventional molecular methods, impeding detailed functional studies that require the information of genomic location. Recently, new technologies are emerging to resolve the positions of varied modifications on both DNA and RNA. Intriguingly, by integrating regional targeting tools and effector proteins, researchers begin to actively control the modification status of desired gene in vivo. In this review, we summarize the characteristics of DNA and RNA modifications, the available mapping and editing tools, and the potential application as well as deficiency of these technologies in basic and translational researches.
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Affiliation(s)
| | | | - Guan-Zheng Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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49
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Chitneedi PK, Arranz JJ, Suárez-Vega A, Martínez-Valladares M, Gutiérrez-Gil B. Identification of potential functional variants underlying ovine resistance to gastrointestinal nematode infection by using RNA-Seq. Anim Genet 2020; 51:266-277. [PMID: 31900978 DOI: 10.1111/age.12894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2019] [Indexed: 02/06/2023]
Abstract
In dairy sheep flocks from Mediterranean countries, replacement and adult ewes are the animals most affected by gastrointestinal nematode (GIN) infections. In this study, we have exploited the information derived from an RNA-Seq experiment with the aim of identifying potential causal mutations related to GIN resistance in sheep. Considering the RNA-Seq samples from 12 ewes previously classified as six resistant and six susceptible animals to experimental infection by Teladorsagia circumcincta, we performed a variant calling analysis pipeline using two different types of software, gatk version 3.7 and Samtools version 1.4. The variants commonly identified by the two packages (high-quality variants) within two types of target regions - (i) QTL regions previously reported in sheep for parasite resistance based on SNP-chip or sequencing technology studies and (ii) functional candidate genes selected from gene expression studies related to GIN resistance in sheep - were further characterised to identify mutations with a potential functional impact. Among the genes harbouring these potential functional variants (930 and 553 respectively for the two types of regions), we identified 111 immune-related genes in the QTL regions and 132 immune-related genes from the initially selected candidate genes. For these immune-related genes harbouring potential functional variants, the enrichment analyses performed highlighted significant GO terms related to apoptosis, adhesion and inflammatory response, in relation to the QTL related variants, and significant disease-related terms such as inflammation, adhesion and necrosis, in relation to the initial candidate gene list. Overall, the study provides a valuable list of potential causal mutations that could be considered as candidate causal mutations in relation to GIN resistance in sheep. Future studies should assess the role of these suggested mutations with the aim of identifying genetic markers that could be directly implemented in sheep breeding programmes considering not only production traits, but also functional traits such as resistance to GIN infections.
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Affiliation(s)
- P K Chitneedi
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - A Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - M Martínez-Valladares
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain.,Instituto de Ganadería de Montaña, CSIC-ULE, 24346, Grulleros, León, Spain
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
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50
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Singh A, Jindal AK, Joshi V, Anjani G, Rawat A. An updated review on phenocopies of primary immunodeficiency diseases. Genes Dis 2019; 7:12-25. [PMID: 32181272 PMCID: PMC7063430 DOI: 10.1016/j.gendis.2019.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 09/04/2019] [Indexed: 02/07/2023] Open
Abstract
Primary immunodeficiency diseases (PIDs) refer to a heterogenous group of disorders characterized clinically by increased susceptibility to infections, autoimmunity and increased risk of malignancies. These group of disorders present with clinical manifestations similar to PIDs with known genetic defects but have either no genetic defect or have a somatic mutation and thus have been labelled as “Phenocopies of PIDs”. These diseases have been further subdivided into those associated with somatic mutations and those associated with presence of auto-antibodies against various cytokines. In this review, we provide an update on clinical manifestations, diagnosis and management of these diseases.
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Affiliation(s)
- Ankita Singh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ankur K Jindal
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Vibhu Joshi
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Gummadi Anjani
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Rawat
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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